Date: 2019-10-15
R version: 3.5.0
*Corresponding author: matthew.malishev@gmail.com
This document can be found at https://github.com/darwinanddavis/githubpres
R session info
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 htmltools_0.3.6 yaml_2.2.0 Rcpp_1.0.2 rmarkdown_1.14
[7] knitr_1.23 xfun_0.8 digest_0.6.20 evaluate_0.14
This document showcases why R is dope.
You can write in-line code if you want to differentiate between when you are typing normally or highlighting model parameters, for example.
Equations like this \(t' = \gamma(t - vx/c^{2})\), to appear within text lines.
Create links to your website.
Make footnotes1.
Create quoted text
Pump the bass in the trunk //
It rattled like a baby hand //
Except this toy cost 80 grand //
And I’m crazy tan, from all the places that I’ve been //
Just from writing words with a pen //
Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum (\(\pi\)) and energy (\(Ej\)) having amplitudes \(a(\pi,Ej)\)
\[ \phi n(r,t) = \sum_{i, j} a(p_{i},E_{j}) e^{ \frac{i} {h} (p_{i} \cdot r - E_{j}t) } \]
where, for convenience, we have suppressed the eigenfunction indices in \(\phi n(r,t)\) and \(an(\pi,Ej)\). Using periodic boundary conditions, the normalization of \(\phi n(r,t)\) in (1) yields
\[ \frac {1} {V_{o}T_{o}h^{4}} \int \phi \cdot (r,t) \phi (r,t)d^{3}rdt = \sum a \cdot (p_{i},E_{j})a(p_{i},E_{j}) = 1 \]
.
Figure 1. Example of a stock plot embedded into a PDF from RMarkdown.
require(viridis)
bm <- 0
par(las = 1, bty = "n")
xlim <- c(-5, 5)
ylim <- c(0, 0.5)
set.seed(12)
N <- 2000
rr <- rnorm(N)
rr2 <- rnorm(N^2)
rr3 <- rnorm(N + 0.3)
rrd <- density(rr)
rrd2 <- density(rr2)
rrd3 <- density(rr3)
main <- paste0(N, " points but plot better")
xlab <- "Points in space"
if (bm == 1) {
layout(matrix(c(rep(1, 3), 2:4), 2, 3, byrow = TRUE))
sc <- 1
plot(rr, las = 1, bty = "n", col = adjustcolor(viridis(N), 0.5), pch = 20, cex = runif(10, 1, 5),
main = main, xlab = xlab)
for (r in list(rrd, rrd2, rrd3)) {
plot(r, xlim = xlim, ylim = ylim, main = "")
polygon(r, col = adjustcolor(viridis(250)[sc], 0.5), border = viridis(250)[sc])
sc <- sc + 100
}
} else {
par(mfrow = c(1, 1))
plot(rr, las = 1, bty = "n", col = adjustcolor(viridis(N), 0.5), pch = 20, cex = runif(10, 1, 5),
main = main, xlab = xlab)
}Figure 2. Example of a plot with improved graphics and its associated code embedded into a PDF from RMarkdown.
Table 1. Definitions of model parameters for individual hosts and parasites. Dimensions and units: -, dimensionless; cm, centimetres; J, Joules; L, length.
| Parameter | Definition | Dimension (unit) |
|---|---|---|
| L | structural length | cm |
| ee | scaled reserve density | J (cm3) |
| D | host development | — |
| RH | energy in reproduction buffer | J |
R codeif (pck == 1) {
p <- c("rJava", "RNetLogo")
remove.packages(p)
# then install rJava and RNetLogo from source
install.packages("rJava", repos = "https://cran.r-project.org/")
install.packages("RNetLogo", repos = "https://cran.r-project.org/")
}shell/bashecho "Hello Bash!"
pwd # check working dir
git init # initialise gitRMatlab package).b = [4; 9; 2] # Column vector
A = [ 3 4 5;
1 3 1;
3 5 9 ]
x = A \ b # Solve the system Ax = b<!-- links-->
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print(x.split(' '))names(knitr::knit_engines$get()) [1] "awk" "bash" "coffee" "gawk" "groovy" "haskell" "lein" "mysql"
[9] "node" "octave" "perl" "psql" "Rscript" "ruby" "sas" "scala"
[17] "sed" "sh" "stata" "zsh" "highlight" "Rcpp" "tikz" "dot"
[25] "c" "fortran" "fortran95" "asy" "cat" "asis" "stan" "block"
[33] "block2" "js" "css" "sql" "go" "python" "julia" "sass"
[41] "scss"
R!Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University. doi: d34464566.
Malishev, M., Bull, C. M., & Kearney, M. R. (2018). An individual‐based model of ectotherm movement integrating metabolic and microclimatic constraints. Methods in Ecology and Evolution, 9(3), 472-489.
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